The federal minister of fisheries has no discretion when it comes to protecting the critical habitat of B.C.'s southern resident killer whales, the Federal Court of Appeal has ruled.

The precedent-setting case relates to the Species at Risk Act (SARA).

"We are thrilled with the court's decision and we now look forward to the opportunity to get on with the work of actually protecting the whales," remarked Margot Venton, a lawyer with Ecojustice, an environmental law firm that fought the case on behalf of nine environmental groups.

In a statement issued Friday, the Department of Fisheries and Oceans said it would not comment until it had completed a review of the decision.

The case stems from the plight of southern B.C.'s iconic marine mammal. At last count, there were 87 animals left in the southern orca population that lives in and around Vancouver Island and the Southern Gulf Islands. The group was listed as endangered under the Species at Risk Act in 2003.

Fisheries and Oceans came up with a plan to protect the whales and their critical habitat, but left certain elements up to the discretion of the minister.

The court said all elements of the plan must be enshrined in law. That would mean protecting chinook salmon, the whales' main food source, reducing underwater noise from boat, industrial and military activity and cleaning up toxic contamination in the whales' home ecosystem.

Species at Risk Act a 'blunt instrument'

The court ruling could cause problems for B.C.'s sport fishermen. A large part of the whale's diet is chinook salmon and some of those fish may have to be set aside for the whales.

"The need to ensure that killer whales have an adequate diet is a tricky issue," said Gerry Kristianson, chair of the Sport Fishing Advisory Board and a Pacific salmon commissioner. He argues that reducing the sport harvest of chinook doesn't mean that orcas will necessarily benefit.

But Kristianson said he wasn't surprised by the court's decision and he expressed sympathy for the federal department.

"SARA is a blunt instrument," he said, adding he believes Fisheries and Oceans was trying to live up to the spirit of SARA. The problem is that whoever drafted SARA wasn't thinking of the implications for marine animals, Kristianson said.

Kristianson cited the noise pollution example.

"Will this require them to stop ferry traffic between the mainland and Vancouver Island?"

On the other hand, commercial fishermen are happy with the decision.

"There are a lot of things that we would need to be doing to protect killer whales that would affect other areas of the sea," said David Lane, the environment director for the United Fishermen and Allied Workers Union.

Lane said dealing with pollution in the southern resident orcas' home would benefit all species in the area. Chinook salmon is not a commercial fish species.

Fisheries and Oceans can seek leave to appeal the decision to the Supreme Court of Canada.